Metagenomic biomarker discovery and explanation
Nicola Segata,Jacques Izard,Jacques Izard,Levi Waldron,Dirk Gevers,Larisa Miropolsky,Wendy S. Garrett,Curtis Huttenhower +7 more
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TLDR
A new method for metagenomic biomarker discovery is described and validates by way of class comparison, tests of biological consistency and effect size estimation to address the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities.Abstract:
This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.read more
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Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut.
Kern Rei Chng,Tarini Shankar Ghosh,Tarini Shankar Ghosh,Yi Han Tan,Tannistha Nandi,Ivor Russel Lee,Amanda Hui Qi Ng,Chenhao Li,Aarthi Ravikrishnan,Kar Mun Lim,David C. Lye,Timothy Barkham,Karthik Raman,Karthik Raman,Swaine L. Chen,Louis Yi Ann Chai,Louis Yi Ann Chai,Barnaby Edward Young,Barnaby Edward Young,Yunn-Hwen Gan,Niranjan Nagarajan,Niranjan Nagarajan +21 more
TL;DR: Functional and growth-rate analysis showed that recovery is supported by enrichment in specific carbohydrate-degradation and energy-production pathways, and the identification of specific species and metabolic functions promoting recovery opens up opportunities for rationally determining pre- and probiotic formulations offering protection from long-term consequences of frequent antibiotic usage.
Journal ArticleDOI
Gut microbiome composition differences among breeds impact feed efficiency in swine
Matteo Bergamaschi,Francesco Tiezzi,Jeremy Howard,Yijian Huang,Kent A. Gray,Constantino Schillebeeckx,Nathan P. McNulty,Christian Maltecca +7 more
TL;DR: Amplicon sequence variants from multiple genera were found to be significantly associated with feed efficiency, regardless of the time point considered, which suggests that the microbial community may contribute to shaping host productive parameters.
Journal ArticleDOI
Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis
Ying He,Tomasz Kosciolek,Jinsong Tang,Yao Zhou,Zongchang Li,Xiaoqian Ma,Qiyun Zhu,Ning Yuan,Liu Yuan,Chunwang Li,Ke Jin,Rob Knight,Ming T. Tsuang,Xiaogang Chen +13 more
TL;DR: Both gut microbiome and imaging studies of UHR subjects suggest the membrane dysfunction in the brain and hence might support the membrane hypothesis of schizophrenia.
Journal ArticleDOI
Dysbiosis, gut barrier dysfunction and inflammation in dementia: a pilot study
Vanessa Stadlbauer,Lara Engertsberger,Irina Komarova,Nicole Feldbacher,Bettina Leber,Gerald Pichler,Nicole Fink,Monika Scarpatetti,Walter Schippinger,Reinhold Schmidt,Angela Horvath +10 more
TL;DR: Dementia is associated with changes in gut microbiome composition and increased biomarkers of gut permeability and inflammation, and Lachnospiraceae NK4A136 group as potential butyrate producer was reduced in dementia.
Journal ArticleDOI
Dynamic change of bacterial community during dairy manure composting process revealed by high-throughput sequencing and advanced bioinformatics tools.
TL;DR: Predicted metagenomics analysis showed that the relative abundance of amino acid, lipid, energy and xenobiotics metabolism increased during the composting process, providing valuable insights into the microbiota during dairy manure composting.
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